rs1426479

Positions:

• chr7-136222069-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435996.1(ENSG00000232053):​n.242+44656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,146 control chromosomes in the GnomAD database, including 6,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6820 hom., cov: 33)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716

Genes affected

ENSG00000232053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375523	NR_187952.1	n.113-20081G>A		intron_variant
LOC105375523	NR_187953.1	n.315-20081G>A		intron_variant
LOC105375523	NR_187954.1	n.421-20081G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000232053	ENST00000435996.1	n.242+44656G>A		intron_variant		3
ENSG00000232053	ENST00000445293.6	n.393-20081G>A		intron_variant		5
ENSG00000232053	ENST00000657456.1	n.287-20081G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43687 AN: 152028 Hom.: 6816 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.277

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.287 AC: 43701 AN: 152146 Hom.: 6820 Cov.: 33 AF XY: 0.290 AC XY: 21560 AN XY: 74380

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.273

Alfa AF: 0.323 Hom.: 16704

Bravo AF: 0.267

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.29
DANN	Benign	0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1426479; hg19: chr7-135906817;